Please note this advice: http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format You definitely do *not* want to convert BAMs to BEDs. That would be a step backwards. BAM files should display in the genome browser without difficulty, unless they are attempting to display pile-ups of thousands of reads in the same location. In this case you want to use the samtools functions to construct bigWig pile-up density graphs from your BAM files. BAM files can display from a URL to your file, you do not need to upload them to the genome browser. They are very efficient when used in this manner. --Hiram ----- Original Message ----- From: "Trent Fowler" <Trent.Fowler@tufts.edu> To: galaxy-user@bx.psu.edu Sent: Tuesday, May 29, 2012 11:57:31 AM Subject: [galaxy-user] Genome Browser Histogram Visualization of Accepted Hits Hello, I am attempting to run accepted hit data from Tophat output into the UCSC Genome Web Browser for visualization of sequencing hits in specific genes. However, the BAM files yield tiles and are too large to present through the browser. Is there a better file format to convert to that would allow better visualization such as histograms?
From word of mouth, I have been told to convert BAMs to BEDs and put BED files through the browser. However, I notice that Galaxy does not have an option for this and the oft used BEDtools appears to involve writing code, which is above my computer abilities.
Any tips or solutions on how to obtain histograms from sequencing data would be very welcome. Thanks Trent Fowler